Fix for # 100 - Remove model library and access

.Rbuildignore

@@ -13,4 +13,5 @@
 ^scratch.R
 ^doc$
 ^Meta$
-^CITATION\.cff$
+^CITATION\.cff$
+^.vscode$

.gitignore

@@ -62,3 +62,4 @@ scratch*
 /Meta/
 
 /.luarc.json
+.vscode

NAMESPACE

@@ -7,7 +7,6 @@ S3method(print,infection)
 S3method(print,intervention)
 S3method(print,population)
 S3method(print,vaccination)
-export(add_to_library)
 export(as.intervention)
 export(as.vaccination)
 export(epidemic_default_cpp)
@@ -16,7 +15,6 @@ export(epidemic_ebola_r)
 export(epidemic_size)
 export(epidemic_vacamole_cpp)
 export(epidemic_vacamole_r)
-export(get_model_names)
 export(get_parameter)
 export(get_transmission_rate)
 export(infection)
@@ -27,7 +25,6 @@ export(is_intervention)
 export(is_population)
 export(is_rate_intervention)
 export(is_vaccination)
-export(model_library)
 export(new_infections)
 export(no_contacts_intervention)
 export(no_rate_intervention)

R/RcppExports.R

@@ -41,8 +41,16 @@
 #' as specified in the initial conditions matrix (see [population()]).
 #' The second list element is a vector of timesteps.
 #' @keywords internal
-.epidemic_default_cpp <- function(initial_state, beta, alpha, gamma, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions, time_dependence, time_end = 100.0, increment = 1.0) {
-    .Call(`_epidemics_epidemic_default_cpp_internal`, initial_state, beta, alpha, gamma, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions, time_dependence, time_end, increment)
+.epidemic_default_cpp <- function(
+    initial_state, beta, alpha, gamma, contact_matrix, npi_time_begin,
+    npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu,
+    rate_interventions, time_dependence, time_end = 100.0, increment = 1.0) {
+    .Call(
+        `_epidemics_epidemic_default_cpp_internal`, initial_state,
+        beta, alpha, gamma, contact_matrix, npi_time_begin, npi_time_end,
+        npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions,
+        time_dependence, time_end, increment
+    )
 }
 
 #' @title Run an SEIR model with Erlang passage times
@@ -73,8 +81,13 @@
 #' This output is intended to be passed to [output_to_df()] to be converted
 #' into a data.frame for further analysis.
 #' @keywords internal
-.epidemic_ebola_cpp <- function(initial_state, population_size, beta, shape_E, rate_E, shape_I, rate_I, time_end) {
-    .Call(`_epidemics_epidemic_ebola_cpp_internal`, initial_state, population_size, beta, shape_E, rate_E, shape_I, rate_I, time_end)
+.epidemic_ebola_cpp <- function(
+    initial_state, population_size, beta, shape_E, rate_E,
+    shape_I, rate_I, time_end) {
+    .Call(
+        `_epidemics_epidemic_ebola_cpp_internal`, initial_state,
+        population_size, beta, shape_E, rate_E, shape_I, rate_I, time_end
+    )
 }
 
 #' @title Run the RIVM Vacamole model
@@ -132,8 +145,17 @@
 #' as specified in the initial conditions matrix (see [population()]).
 #' The second list element is a vector of timesteps.
 #' @keywords internal
-.epidemic_vacamole_cpp <- function(initial_state, beta, beta_v, alpha, omega, omega_v, eta, eta_v, gamma, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions, time_dependence, time_end = 100.0, increment = 1.0) {
-    .Call(`_epidemics_epidemic_vacamole_cpp_internal`, initial_state, beta, beta_v, alpha, omega, omega_v, eta, eta_v, gamma, contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end, vax_nu, rate_interventions, time_dependence, time_end, increment)
+.epidemic_vacamole_cpp <- function(
+    initial_state, beta, beta_v, alpha, omega, omega_v, eta, eta_v, gamma,
+    contact_matrix, npi_time_begin, npi_time_end, npi_cr, vax_time_begin,
+    vax_time_end, vax_nu, rate_interventions, time_dependence,
+    time_end = 100.0, increment = 1.0) {
+    .Call(
+        `_epidemics_epidemic_vacamole_cpp_internal`, initial_state,
+        beta, beta_v, alpha, omega, omega_v, eta, eta_v, gamma, contact_matrix,
+        npi_time_begin, npi_time_end, npi_cr, vax_time_begin, vax_time_end,
+        vax_nu, rate_interventions, time_dependence, time_end, increment
+    )
 }
 
 #' @title Compute the discrete probability of the truncated Erlang distribution
@@ -143,4 +165,3 @@
 prob_discrete_erlang_cpp <- function(shape, rate) {
     .Call(`_epidemics_prob_discrete_erlang_cpp`, shape, rate)
 }
-

R/check_args_default.R

@@ -65,8 +65,8 @@
   )
 
   # load number of compartments to check initial conditions matrix
-  compartments_default <- read_from_library(
-    model_name = "default", what = "compartments"
+  compartments_default <- c(
+    "susceptible", "exposed", "infectious", "recovered", "vaccinated"
   )
   assert_population(
     mod_args[["population"]],

R/check_args_ebola.R

@@ -43,9 +43,10 @@
   )
 
   # load number of compartments to check initial conditions matrix
-  compartments_ebola <- read_from_library(
-    model_name = "ebola", what = "compartments"
+  compartments_ebola <- c(
+    "susceptible", "exposed", "infectious", "hospitalised", "funeral", "removed"
   )
+
   assert_population(
     mod_args[["population"]],
     compartments = compartments_ebola

R/check_args_vacamole.R

@@ -88,8 +88,10 @@
   )
 
   # load number of compartments to check initial conditions matrix
-  compartments_vacamole <- read_from_library(
-    model_name = "vacamole", what = "compartments"
+  compartments_vacamole <- c(
+    "susceptible", "vaccinated_one_dose", "vaccinated_two_dose",
+    "exposed", "exposed_vaccinated", "infectious", "infectious_vaccinated",
+    "hospitalised", "hospitalised_vaccinated", "dead", "recovered"
   )
   # input checking on population parameters
   assert_population(

R/epidemic_ebola.R

@@ -194,7 +194,6 @@ epidemic_ebola_r <- function(population, infection,
   # input checking for the ebola R model
   assert_population(
     population,
-    demography_groups = 1L,
     compartments = c(
       "susceptible", "exposed", "infectious",
       "hospitalised", "funeral", "removed"